Merge pull request #11669 from rmitsch/feature/candidate-generation-by-docs

Prototype: Entity linking with custom KBs
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Sofie Van Landeghem 2023-04-24 16:35:37 +02:00 committed by GitHub
commit 178f259dbd
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14 changed files with 501 additions and 291 deletions

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@ -30,7 +30,6 @@ MOD_NAMES = [
"spacy.lexeme",
"spacy.vocab",
"spacy.attrs",
"spacy.kb.candidate",
"spacy.kb.kb",
"spacy.kb.kb_in_memory",
"spacy.ml.parser_model",

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@ -957,11 +957,10 @@ class Errors(metaclass=ErrorsWithCodes):
"case pass an empty list for the previously not specified argument to avoid this error.")
E1043 = ("Expected None or a value in range [{range_start}, {range_end}] for entity linker threshold, but got "
"{value}.")
E1044 = ("Expected `candidates_batch_size` to be >= 1, but got: {value}")
E1045 = ("Encountered {parent} subclass without `{parent}.{method}` "
E1044 = ("Encountered {parent} subclass without `{parent}.{method}` "
"method in '{name}'. If you want to use this method, make "
"sure it's overwritten on the subclass.")
E1046 = ("{cls_name} is an abstract class and cannot be instantiated. If you are looking for spaCy's default "
E1045 = ("{cls_name} is an abstract class and cannot be instantiated. If you are looking for spaCy's default "
"knowledge base, use `InMemoryLookupKB`.")
E1047 = ("`find_threshold()` only supports components with a `scorer` attribute.")
E1048 = ("Got '{unexpected}' as console progress bar type, but expected one of the following: {expected}")

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@ -1,3 +1,5 @@
from .kb import KnowledgeBase
from .kb_in_memory import InMemoryLookupKB
from .candidate import Candidate, get_candidates, get_candidates_batch
from .candidate import Candidate
__all__ = ["KnowledgeBase", "InMemoryLookupKB", "Candidate"]

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@ -1,12 +0,0 @@
from .kb cimport KnowledgeBase
from libcpp.vector cimport vector
from ..typedefs cimport hash_t
# Object used by the Entity Linker that summarizes one entity-alias candidate combination.
cdef class Candidate:
cdef readonly KnowledgeBase kb
cdef hash_t entity_hash
cdef float entity_freq
cdef vector[float] entity_vector
cdef hash_t alias_hash
cdef float prior_prob

109
spacy/kb/candidate.py Normal file
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@ -0,0 +1,109 @@
import abc
from typing import List, Union, Callable
class BaseCandidate(abc.ABC):
"""A `BaseCandidate` object refers to a textual mention (`alias`) that may or may not be resolved
to a specific `entity_id` from a Knowledge Base. This will be used as input for the entity_id linking
algorithm which will disambiguate the various candidates to the correct one.
Each candidate (alias, entity_id) pair is assigned a certain prior probability.
DOCS: https://spacy.io/api/kb/#candidate-init
"""
def __init__(
self, mention: str, entity_id: Union[int, str], entity_vector: List[float]
):
"""Create new instance of `Candidate`. Note: has to be a sub-class, otherwise error will be raised.
mention (str): Mention text for this candidate.
entity_id (Union[int, str]): Unique entity ID.
entity_vector (List[float]): Entity embedding.
"""
self._mention = mention
self._entity_id = entity_id
self._entity_vector = entity_vector
@property
def entity(self) -> Union[int, str]:
"""RETURNS (Union[int, str]): Entity ID."""
return self._entity_id
@property
@abc.abstractmethod
def entity_(self) -> str:
"""RETURNS (str): Entity name."""
@property
def mention(self) -> str:
"""RETURNS (str): Mention."""
return self._mention
@property
def entity_vector(self) -> List[float]:
"""RETURNS (List[float]): Entity vector."""
return self._entity_vector
class Candidate(BaseCandidate):
"""`Candidate` for InMemoryLookupKBCandidate."""
def __init__(
self,
retrieve_string_from_hash: Callable[[int], str],
entity_hash: int,
entity_freq: int,
entity_vector: List[float],
alias_hash: int,
prior_prob: float,
):
"""
retrieve_string_from_hash (Callable[[int], str]): Callable retrieveing entity name from provided entity/vocab
hash.
entity_hash (str): Hashed entity name /ID.
entity_freq (int): Entity frequency in KB corpus.
entity_vector (List[float]): Entity embedding.
alias_hash (int): Hashed alias.
prior_prob (float): Prior probability of entity for this mention - i.e. the probability that, independent of
the context, this mention resolves to this entity_id in the corpus used to build the knowledge base. In
cases in which this isn't always possible (e.g.: the corpus to analyse contains mentions that the KB corpus
doesn't) it might be better to eschew this information and always supply the same value.
"""
super().__init__(
mention=retrieve_string_from_hash(alias_hash),
entity_id=entity_hash,
entity_vector=entity_vector,
)
self._retrieve_string_from_hash = retrieve_string_from_hash
self._entity_hash = entity_hash
self._entity_freq = entity_freq
self._alias_hash = alias_hash
self._prior_prob = prior_prob
@property
def entity(self) -> int:
"""RETURNS (int): hash of the entity_id's KB ID/name"""
return self._entity_hash
@property
def entity_(self) -> str:
"""RETURNS (str): ID/name of this entity_id in the KB"""
return self._retrieve_string_from_hash(self._entity_hash)
@property
def alias(self) -> int:
"""RETURNS (int): hash of the alias"""
return self._alias_hash
@property
def alias_(self) -> str:
"""RETURNS (str): ID of the original alias"""
return self._retrieve_string_from_hash(self._alias_hash)
@property
def entity_freq(self) -> float:
return self._entity_freq
@property
def prior_prob(self) -> float:
"""RETURNS (List[float]): Entity vector."""
return self._prior_prob

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@ -1,74 +0,0 @@
# cython: infer_types=True, profile=True
from typing import Iterable
from .kb cimport KnowledgeBase
from ..tokens import Span
cdef class Candidate:
"""A `Candidate` object refers to a textual mention (`alias`) that may or may not be resolved
to a specific `entity` from a Knowledge Base. This will be used as input for the entity linking
algorithm which will disambiguate the various candidates to the correct one.
Each candidate (alias, entity) pair is assigned a certain prior probability.
DOCS: https://spacy.io/api/kb/#candidate-init
"""
def __init__(self, KnowledgeBase kb, entity_hash, entity_freq, entity_vector, alias_hash, prior_prob):
self.kb = kb
self.entity_hash = entity_hash
self.entity_freq = entity_freq
self.entity_vector = entity_vector
self.alias_hash = alias_hash
self.prior_prob = prior_prob
@property
def entity(self) -> int:
"""RETURNS (uint64): hash of the entity's KB ID/name"""
return self.entity_hash
@property
def entity_(self) -> str:
"""RETURNS (str): ID/name of this entity in the KB"""
return self.kb.vocab.strings[self.entity_hash]
@property
def alias(self) -> int:
"""RETURNS (uint64): hash of the alias"""
return self.alias_hash
@property
def alias_(self) -> str:
"""RETURNS (str): ID of the original alias"""
return self.kb.vocab.strings[self.alias_hash]
@property
def entity_freq(self) -> float:
return self.entity_freq
@property
def entity_vector(self) -> Iterable[float]:
return self.entity_vector
@property
def prior_prob(self) -> float:
return self.prior_prob
def get_candidates(kb: KnowledgeBase, mention: Span) -> Iterable[Candidate]:
"""
Return candidate entities for a given mention and fetching appropriate entries from the index.
kb (KnowledgeBase): Knowledge base to query.
mention (Span): Entity mention for which to identify candidates.
RETURNS (Iterable[Candidate]): Identified candidates.
"""
return kb.get_candidates(mention)
def get_candidates_batch(kb: KnowledgeBase, mentions: Iterable[Span]) -> Iterable[Iterable[Candidate]]:
"""
Return candidate entities for the given mentions and fetching appropriate entries from the index.
kb (KnowledgeBase): Knowledge base to query.
mention (Iterable[Span]): Entity mentions for which to identify candidates.
RETURNS (Iterable[Iterable[Candidate]]): Identified candidates.
"""
return kb.get_candidates_batch(mentions)

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@ -7,4 +7,4 @@ from ..vocab cimport Vocab
cdef class KnowledgeBase:
cdef Pool mem
cdef readonly Vocab vocab
cdef readonly int64_t entity_vector_length
cdef public int64_t entity_vector_length

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@ -1,11 +1,11 @@
# cython: infer_types=True, profile=True
from pathlib import Path
from typing import Iterable, Tuple, Union
from typing import Iterable, Tuple, Union, Iterator, TypeVar, Type, Callable
from cymem.cymem cimport Pool
from .candidate import Candidate
from ..tokens import Span
from ..tokens import Span, SpanGroup, Doc
from ..util import SimpleFrozenList
from ..errors import Errors
@ -18,38 +18,52 @@ cdef class KnowledgeBase:
DOCS: https://spacy.io/api/kb
"""
_KBType = TypeVar("_KBType", bound=KnowledgeBase)
def __init__(self, vocab: Vocab, entity_vector_length: int):
"""Create a KnowledgeBase."""
# Make sure abstract KB is not instantiated.
if self.__class__ == KnowledgeBase:
raise TypeError(
Errors.E1046.format(cls_name=self.__class__.__name__)
Errors.E1045.format(cls_name=self.__class__.__name__)
)
self.vocab = vocab
self.entity_vector_length = entity_vector_length
self.mem = Pool()
def get_candidates_batch(self, mentions: Iterable[Span]) -> Iterable[Iterable[Candidate]]:
def get_candidates_all(self, mentions: Iterator[SpanGroup]) -> Iterator[Iterable[Iterable[Candidate]]]:
"""
Return candidate entities for specified texts. Each candidate defines the entity, the original alias,
and the prior probability of that alias resolving to that entity.
If no candidate is found for a given text, an empty list is returned.
mentions (Iterable[Span]): Mentions for which to get candidates.
RETURNS (Iterable[Iterable[Candidate]]): Identified candidates.
Return candidate entities for mentions stored in `ent` attribute in passed docs. Each candidate defines the
entity, the original alias, and the prior probability of that alias resolving to that entity.
If no candidate is found for a given mention, an empty list is returned.
mentions (Iterator[SpanGroup]): Mentions per doc as SpanGroup instance.
RETURNS (Iterator[Iterable[Iterable[Candidate]]]): Identified candidates per document.
"""
for doc_mentions in mentions:
yield [self.get_candidates(ent_span) for ent_span in doc_mentions]
@staticmethod
def get_ents_as_spangroup(doc: Doc, extractor: Union[str, Callable[[Iterable[Span]], Doc]] = "ent") -> SpanGroup:
"""
Fetch entities from doc and returns them as a SpanGroup ready to be used in
`KnowledgeBase.get_candidates_all()`.
doc (Doc): Doc whose entities should be fetched.
extractor (Union[str, Callable[[Iterable[Span]], Doc]]): Defines how to retrieve object holding spans
used to describe entities. This can be a key referring to a property of the doc instance (e.g. "
"""
return [self.get_candidates(span) for span in mentions]
def get_candidates(self, mention: Span) -> Iterable[Candidate]:
"""
Return candidate entities for specified text. Each candidate defines the entity, the original alias,
and the prior probability of that alias resolving to that entity.
If the no candidate is found for a given text, an empty list is returned.
Note that doc is not utilized for further context in this implementation.
mention (Span): Mention for which to get candidates.
RETURNS (Iterable[Candidate]): Identified candidates.
"""
raise NotImplementedError(
Errors.E1045.format(parent="KnowledgeBase", method="get_candidates", name=self.__name__)
Errors.E1044.format(parent="KnowledgeBase", method="get_candidates", name=self.__name__)
)
def get_vectors(self, entities: Iterable[str]) -> Iterable[Iterable[float]]:
@ -67,7 +81,7 @@ cdef class KnowledgeBase:
RETURNS (Iterable[float]): Vector for specified entity.
"""
raise NotImplementedError(
Errors.E1045.format(parent="KnowledgeBase", method="get_vector", name=self.__name__)
Errors.E1044.format(parent="KnowledgeBase", method="get_vector", name=self.__name__)
)
def to_bytes(self, **kwargs) -> bytes:
@ -75,7 +89,7 @@ cdef class KnowledgeBase:
RETURNS (bytes): Current state as binary string.
"""
raise NotImplementedError(
Errors.E1045.format(parent="KnowledgeBase", method="to_bytes", name=self.__name__)
Errors.E1044.format(parent="KnowledgeBase", method="to_bytes", name=self.__name__)
)
def from_bytes(self, bytes_data: bytes, *, exclude: Tuple[str] = tuple()):
@ -84,25 +98,45 @@ cdef class KnowledgeBase:
exclude (Tuple[str]): Properties to exclude when restoring KB.
"""
raise NotImplementedError(
Errors.E1045.format(parent="KnowledgeBase", method="from_bytes", name=self.__name__)
Errors.E1044.format(parent="KnowledgeBase", method="from_bytes", name=self.__name__)
)
def to_disk(self, path: Union[str, Path], exclude: Iterable[str] = SimpleFrozenList()) -> None:
"""
Write KnowledgeBase content to disk.
"""Write KnowledgeBase content to disk.
path (Union[str, Path]): Target file path.
exclude (Iterable[str]): List of components to exclude.
"""
raise NotImplementedError(
Errors.E1045.format(parent="KnowledgeBase", method="to_disk", name=self.__name__)
Errors.E1044.format(parent="KnowledgeBase", method="to_disk", name=self.__name__)
)
def from_disk(self, path: Union[str, Path], exclude: Iterable[str] = SimpleFrozenList()) -> None:
"""
Load KnowledgeBase content from disk.
"""Load KnowledgeBase content from disk.
path (Union[str, Path]): Target file path.
exclude (Iterable[str]): List of components to exclude.
"""
raise NotImplementedError(
Errors.E1045.format(parent="KnowledgeBase", method="from_disk", name=self.__name__)
Errors.E1044.format(parent="KnowledgeBase", method="from_disk", name=self.__name__)
)
@classmethod
def generate_from_disk(
cls: Type[_KBType], path: Union[str, Path], exclude: Iterable[str] = SimpleFrozenList()
) -> _KBType:
"""
Factory method for generating KnowledgeBase subclass instance from file.
path (Union[str, Path]): Target file path.
exclude (Iterable[str]): List of components to exclude.
return (_KBType): Instance of KnowledgeBase subclass generated from file.
"""
raise NotImplementedError(
Errors.E1044.format(parent="KnowledgeBase", method="generate_from_disk", name=cls.__name__)
)
def __len__(self) -> int:
"""Returns number of entities in the KnowledgeBase.
RETURNS (int): Number of entities in the KnowledgeBase.
"""
raise NotImplementedError(
Errors.E1044.format(parent="KnowledgeBase", method="__len__", name=self.__name__)
)

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@ -1,5 +1,5 @@
# cython: infer_types=True, profile=True
from typing import Iterable, Callable, Dict, Any, Union
from typing import Iterable, Callable, Dict, Any, Union, Optional
import srsly
from preshed.maps cimport PreshMap
@ -11,7 +11,7 @@ from libcpp.vector cimport vector
from pathlib import Path
import warnings
from ..tokens import Span
from ..tokens import Span, Doc
from ..typedefs cimport hash_t
from ..errors import Errors, Warnings
from .. import util
@ -49,6 +49,14 @@ cdef class InMemoryLookupKB(KnowledgeBase):
def is_empty(self):
return len(self) == 0
@classmethod
def generate_from_disk(
cls, path: Union[str, Path], exclude: Iterable[str] = SimpleFrozenList()
) -> "InMemoryLookupKB":
kb = InMemoryLookupKB(vocab=Vocab(strings=["."]), entity_vector_length=1)
kb.from_disk(path)
return kb
def __len__(self):
return self.get_size_entities()
@ -227,7 +235,7 @@ cdef class InMemoryLookupKB(KnowledgeBase):
self._aliases_table[alias_index] = alias_entry
def get_candidates(self, mention: Span) -> Iterable[Candidate]:
return self.get_alias_candidates(mention.text) # type: ignore
return self.get_alias_candidates(mention.text)
def get_alias_candidates(self, str alias) -> Iterable[Candidate]:
"""
@ -241,14 +249,18 @@ cdef class InMemoryLookupKB(KnowledgeBase):
alias_index = <int64_t>self._alias_index.get(alias_hash)
alias_entry = self._aliases_table[alias_index]
return [Candidate(kb=self,
entity_hash=self._entries[entry_index].entity_hash,
entity_freq=self._entries[entry_index].freq,
entity_vector=self._vectors_table[self._entries[entry_index].vector_index],
alias_hash=alias_hash,
prior_prob=prior_prob)
for (entry_index, prior_prob) in zip(alias_entry.entry_indices, alias_entry.probs)
if entry_index != 0]
return [
Candidate(
retrieve_string_from_hash=self.vocab.strings.__getitem__,
entity_hash=self._entries[entry_index].entity_hash,
entity_freq=self._entries[entry_index].freq,
entity_vector=self._vectors_table[self._entries[entry_index].vector_index],
alias_hash=alias_hash,
prior_prob=prior_prob
)
for (entry_index, prior_prob) in zip(alias_entry.entry_indices, alias_entry.probs)
if entry_index != 0
]
def get_vector(self, str entity):
cdef hash_t entity_hash = self.vocab.strings[entity]

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@ -1,14 +1,14 @@
from pathlib import Path
from typing import Optional, Callable, Iterable, List, Tuple
from typing import Optional, Callable, Iterable, List, Tuple, Iterator
from thinc.types import Floats2d
from thinc.api import chain, list2ragged, reduce_mean, residual
from thinc.api import Model, Maxout, Linear, tuplify, Ragged
from ...util import registry
from ...kb import KnowledgeBase, InMemoryLookupKB
from ...kb import Candidate, get_candidates, get_candidates_batch
from ...kb import Candidate
from ...vocab import Vocab
from ...tokens import Span, Doc
from ...tokens import Span, Doc, SpanGroup
from ..extract_spans import extract_spans
from ...errors import Errors
@ -89,14 +89,6 @@ def load_kb(
return kb_from_file
@registry.misc("spacy.EmptyKB.v2")
def empty_kb_for_config() -> Callable[[Vocab, int], KnowledgeBase]:
def empty_kb_factory(vocab: Vocab, entity_vector_length: int):
return InMemoryLookupKB(vocab=vocab, entity_vector_length=entity_vector_length)
return empty_kb_factory
@registry.misc("spacy.EmptyKB.v1")
def empty_kb(
entity_vector_length: int,
@ -107,13 +99,44 @@ def empty_kb(
return empty_kb_factory
@registry.misc("spacy.EmptyKB.v2")
def empty_kb_for_config() -> Callable[[Vocab, int], KnowledgeBase]:
def empty_kb_factory(vocab: Vocab, entity_vector_length: int):
return InMemoryLookupKB(vocab=vocab, entity_vector_length=entity_vector_length)
return empty_kb_factory
def get_candidates(kb: KnowledgeBase, mention: Span) -> Iterable[Candidate]:
"""
Return candidate entities for a given mention and fetching appropriate entries from the index.
kb (KnowledgeBase): Knowledge base to query.
mention (Span): Entity mention for which to identify candidates.
RETURNS (Iterable[Candidate]): Identified candidates.
"""
return kb.get_candidates(mention)
def get_candidates_all(
kb: KnowledgeBase, mentions: Iterator[SpanGroup]
) -> Iterator[Iterable[Iterable[Candidate]]]:
"""
Return candidate entities for the given mentions and fetching appropriate entries from the index.
kb (KnowledgeBase): Knowledge base to query.
mentions (Iterator[SpanGroup]): Mentions per doc as SpanGroup instance.
RETURNS (Iterator[Iterable[Iterable[Candidate]]]): Identified candidates per document.
"""
return kb.get_candidates_all(mentions)
@registry.misc("spacy.CandidateGenerator.v1")
def create_candidates() -> Callable[[KnowledgeBase, Span], Iterable[Candidate]]:
return get_candidates
@registry.misc("spacy.CandidateBatchGenerator.v1")
def create_candidates_batch() -> Callable[
[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]
@registry.misc("spacy.CandidateAllGenerator.v1")
def create_candidates_all() -> Callable[
[KnowledgeBase, Iterator[SpanGroup]],
Iterator[Iterable[Iterable[Candidate]]],
]:
return get_candidates_batch
return get_candidates_all

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@ -1,4 +1,13 @@
from typing import Optional, Iterable, Callable, Dict, Union, List, Any
from typing import (
Optional,
Iterable,
Callable,
Dict,
Union,
List,
Any,
Iterator,
)
from thinc.types import Floats2d
from pathlib import Path
from itertools import islice
@ -8,8 +17,7 @@ from thinc.api import CosineDistance, Model, Optimizer, Config
from thinc.api import set_dropout_rate
from ..kb import KnowledgeBase, Candidate
from ..ml import empty_kb
from ..tokens import Doc, Span
from ..tokens import Doc, Span, SpanGroup
from .pipe import deserialize_config
from .legacy.entity_linker import EntityLinker_v1
from .trainable_pipe import TrainablePipe
@ -53,12 +61,12 @@ DEFAULT_NEL_MODEL = Config().from_str(default_model_config)["model"]
"incl_context": True,
"entity_vector_length": 64,
"get_candidates": {"@misc": "spacy.CandidateGenerator.v1"},
"get_candidates_batch": {"@misc": "spacy.CandidateBatchGenerator.v1"},
"get_candidates_all": {"@misc": "spacy.CandidateAllGenerator.v1"},
"generate_empty_kb": {"@misc": "spacy.EmptyKB.v2"},
"overwrite": True,
"scorer": {"@scorers": "spacy.entity_linker_scorer.v1"},
"use_gold_ents": True,
"candidates_batch_size": 1,
"candidates_doc_mode": False,
"threshold": None,
},
default_score_weights={
@ -78,14 +86,14 @@ def make_entity_linker(
incl_context: bool,
entity_vector_length: int,
get_candidates: Callable[[KnowledgeBase, Span], Iterable[Candidate]],
get_candidates_batch: Callable[
[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]
get_candidates_all: Callable[
[KnowledgeBase, Iterator[SpanGroup]], Iterator[Iterable[Iterable[Candidate]]]
],
generate_empty_kb: Callable[[Vocab, int], KnowledgeBase],
overwrite: bool,
scorer: Optional[Callable],
use_gold_ents: bool,
candidates_batch_size: int,
candidates_doc_mode: bool,
threshold: Optional[float] = None,
):
"""Construct an EntityLinker component.
@ -98,16 +106,18 @@ def make_entity_linker(
incl_prior (bool): Whether or not to include prior probabilities from the KB in the model.
incl_context (bool): Whether or not to include the local context in the model.
entity_vector_length (int): Size of encoding vectors in the KB.
get_candidates (Callable[[KnowledgeBase, Span], Iterable[Candidate]]): Function that
produces a list of candidates, given a certain knowledge base and a textual mention.
get_candidates_batch (
Callable[[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]], Iterable[Candidate]]
): Function that produces a list of candidates, given a certain knowledge base and several textual mentions.
get_candidates (Callable[[KnowledgeBase, Span], Iterable[Candidate]]): Function producing a list of
candidates, given a certain knowledge base and a textual mention.
get_candidates_all (Callable[[KnowledgeBase, Iterator[SpanGroup]], Iterator[Iterable[Iterable[Candidate]]]]):
Function producing a list of candidates per document, given a certain knowledge base and several textual
documents with textual mentions.
generate_empty_kb (Callable[[Vocab, int], KnowledgeBase]): Callable returning empty KnowledgeBase.
scorer (Optional[Callable]): The scoring method.
use_gold_ents (bool): Whether to copy entities from gold docs or not. If false, another
component must provide entity annotations.
candidates_batch_size (int): Size of batches for entity candidate generation.
candidates_doc_mode (bool): Whether or not to operate candidate generation in doc mode, i.e. to provide a generator
yielding entities per document (candidate generator callable is called only once in this case). If False,
the candidate generator is called once per entity.
threshold (Optional[float]): Confidence threshold for entity predictions. If confidence is below the threshold,
prediction is discarded. If None, predictions are not filtered by any threshold.
"""
@ -137,12 +147,12 @@ def make_entity_linker(
incl_context=incl_context,
entity_vector_length=entity_vector_length,
get_candidates=get_candidates,
get_candidates_batch=get_candidates_batch,
get_candidates_all=get_candidates_all,
generate_empty_kb=generate_empty_kb,
overwrite=overwrite,
scorer=scorer,
use_gold_ents=use_gold_ents,
candidates_batch_size=candidates_batch_size,
candidates_doc_mode=candidates_doc_mode,
threshold=threshold,
)
@ -176,14 +186,15 @@ class EntityLinker(TrainablePipe):
incl_context: bool,
entity_vector_length: int,
get_candidates: Callable[[KnowledgeBase, Span], Iterable[Candidate]],
get_candidates_batch: Callable[
[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]
get_candidates_all: Callable[
[KnowledgeBase, Iterator[SpanGroup]],
Iterator[Iterable[Iterable[Candidate]]],
],
generate_empty_kb: Callable[[Vocab, int], KnowledgeBase],
overwrite: bool = BACKWARD_OVERWRITE,
scorer: Optional[Callable] = entity_linker_score,
use_gold_ents: bool,
candidates_batch_size: int,
candidates_doc_mode: bool,
threshold: Optional[float] = None,
) -> None:
"""Initialize an entity linker.
@ -197,17 +208,18 @@ class EntityLinker(TrainablePipe):
incl_prior (bool): Whether or not to include prior probabilities from the KB in the model.
incl_context (bool): Whether or not to include the local context in the model.
entity_vector_length (int): Size of encoding vectors in the KB.
get_candidates (Callable[[KnowledgeBase, Span], Iterable[Candidate]]): Function that
produces a list of candidates, given a certain knowledge base and a textual mention.
get_candidates_batch (
Callable[[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]],
Iterable[Candidate]]
): Function that produces a list of candidates, given a certain knowledge base and several textual mentions.
get_candidates (Callable[[KnowledgeBase, Span], Iterable[Candidate]]): Function producing a list
of candidates, given a certain knowledge base and a textual mention.
get_candidates_all (Callable[[KnowledgeBase, Iterator[SpanGroup]], Iterator[Iterable[Iterable[Candidate]]]]):
Function producing a list of candidates per document, given a certain knowledge base and several textual
documents with textual mentions.
generate_empty_kb (Callable[[Vocab, int], KnowledgeBase]): Callable returning empty KnowledgeBase.
scorer (Optional[Callable]): The scoring method. Defaults to Scorer.score_links.
use_gold_ents (bool): Whether to copy entities from gold docs or not. If false, another
component must provide entity annotations.
candidates_batch_size (int): Size of batches for entity candidate generation.
candidates_doc_mode (bool): Whether or not to operate candidate generation in doc mode, i.e. to provide a
generator yielding entities per document (candidate generator callable is called only once in this case). If
False, the candidate generator is called once per entity.
threshold (Optional[float]): Confidence threshold for entity predictions. If confidence is below the
threshold, prediction is discarded. If None, predictions are not filtered by any threshold.
DOCS: https://spacy.io/api/entitylinker#init
@ -231,18 +243,16 @@ class EntityLinker(TrainablePipe):
self.incl_prior = incl_prior
self.incl_context = incl_context
self.get_candidates = get_candidates
self.get_candidates_batch = get_candidates_batch
self.get_candidates_all = get_candidates_all
self.generate_empty_kb = generate_empty_kb
self.cfg: Dict[str, Any] = {"overwrite": overwrite}
self.distance = CosineDistance(normalize=False)
self.kb = generate_empty_kb(self.vocab, entity_vector_length)
self.scorer = scorer
self.use_gold_ents = use_gold_ents
self.candidates_batch_size = candidates_batch_size
self.candidates_doc_mode = candidates_doc_mode
self.threshold = threshold
if candidates_batch_size < 1:
raise ValueError(Errors.E1044)
def set_kb(self, kb_loader: Callable[[Vocab], KnowledgeBase]):
"""Define the KB of this pipe by providing a function that will
create it using this object's vocab."""
@ -319,7 +329,6 @@ class EntityLinker(TrainablePipe):
If one isn't present, then the update step needs to be skipped.
"""
for eg in examples:
for ent in eg.predicted.ents:
candidates = list(self.get_candidates(self.kb, ent))
@ -445,108 +454,125 @@ class EntityLinker(TrainablePipe):
return final_kb_ids
if isinstance(docs, Doc):
docs = [docs]
for i, doc in enumerate(docs):
if len(doc) == 0:
docs = list(docs)
# Determine which entities are to be ignored due to labels_discard.
valid_ent_idx_per_doc = (
[
idx
for idx in range(len(doc.ents))
if doc.ents[idx].label_ not in self.labels_discard
]
for doc in docs
if len(doc) and len(doc.ents)
)
# Call candidate generator.
if self.candidates_doc_mode:
all_ent_cands = self.get_candidates_all(
self.kb,
(
SpanGroup(
doc,
spans=[doc.ents[idx] for idx in next(valid_ent_idx_per_doc)],
)
for doc in docs
if len(doc) and len(doc.ents)
),
)
else:
# Alternative: collect entities the old-fashioned way - by retrieving entities individually.
all_ent_cands = (
[
self.get_candidates(self.kb, doc.ents[idx])
for idx in next(valid_ent_idx_per_doc)
]
for doc in docs
if len(doc) and len(doc.ents)
)
for doc_idx, doc in enumerate(docs):
if len(doc) == 0 or len(doc.ents) == 0:
continue
sentences = [s for s in doc.sents]
doc_ent_cands = list(next(all_ent_cands))
# Loop over entities in batches.
for ent_idx in range(0, len(doc.ents), self.candidates_batch_size):
ent_batch = doc.ents[ent_idx : ent_idx + self.candidates_batch_size]
# Look up candidate entities.
valid_ent_idx = [
idx
for idx in range(len(ent_batch))
if ent_batch[idx].label_ not in self.labels_discard
]
batch_candidates = list(
self.get_candidates_batch(
self.kb, [ent_batch[idx] for idx in valid_ent_idx]
)
if self.candidates_batch_size > 1
else [
self.get_candidates(self.kb, ent_batch[idx])
for idx in valid_ent_idx
]
# Looping over candidate entities for this doc. (TODO: rewrite)
for ent_cand_idx, ent in enumerate(doc.ents):
assert hasattr(ent, "sents")
sents = list(ent.sents)
sent_indices = (
sentences.index(sents[0]),
sentences.index(sents[-1]),
)
assert sent_indices[1] >= sent_indices[0] >= 0
# Looping through each entity in batch (TODO: rewrite)
for j, ent in enumerate(ent_batch):
assert hasattr(ent, "sents")
sents = list(ent.sents)
sent_indices = (
sentences.index(sents[0]),
sentences.index(sents[-1]),
if self.incl_context:
# get n_neighbour sentences, clipped to the length of the document
start_sentence = max(0, sent_indices[0] - self.n_sents)
end_sentence = min(
len(sentences) - 1, sent_indices[1] + self.n_sents
)
assert sent_indices[1] >= sent_indices[0] >= 0
if self.incl_context:
# get n_neighbour sentences, clipped to the length of the document
start_sentence = max(0, sent_indices[0] - self.n_sents)
end_sentence = min(
len(sentences) - 1, sent_indices[1] + self.n_sents
)
start_token = sentences[start_sentence].start
end_token = sentences[end_sentence].end
sent_doc = doc[start_token:end_token].as_doc()
# currently, the context is the same for each entity in a sentence (should be refined)
sentence_encoding = self.model.predict([sent_doc])[0]
sentence_encoding_t = sentence_encoding.T
sentence_norm = xp.linalg.norm(sentence_encoding_t)
entity_count += 1
if ent.label_ in self.labels_discard:
# ignoring this entity - setting to NIL
start_token = sentences[start_sentence].start
end_token = sentences[end_sentence].end
sent_doc = doc[start_token:end_token].as_doc()
# currently, the context is the same for each entity in a sentence (should be refined)
sentence_encoding = self.model.predict([sent_doc])[0]
sentence_encoding_t = sentence_encoding.T
sentence_norm = xp.linalg.norm(sentence_encoding_t)
entity_count += 1
if ent.label_ in self.labels_discard:
# ignoring this entity - setting to NIL
final_kb_ids.append(self.NIL)
else:
candidates = list(doc_ent_cands[ent_cand_idx])
if not candidates:
# no prediction possible for this entity - setting to NIL
final_kb_ids.append(self.NIL)
elif len(candidates) == 1 and self.threshold is None:
# shortcut for efficiency reasons: take the 1 candidate
final_kb_ids.append(candidates[0].entity_)
else:
candidates = list(batch_candidates[j])
if not candidates:
# no prediction possible for this entity - setting to NIL
final_kb_ids.append(self.NIL)
elif len(candidates) == 1 and self.threshold is None:
# shortcut for efficiency reasons: take the 1 candidate
final_kb_ids.append(candidates[0].entity_)
else:
random.shuffle(candidates)
# set all prior probabilities to 0 if incl_prior=False
prior_probs = xp.asarray([c.prior_prob for c in candidates])
if not self.incl_prior:
prior_probs = xp.asarray([0.0 for _ in candidates])
scores = prior_probs
# add in similarity from the context
if self.incl_context:
entity_encodings = xp.asarray(
[c.entity_vector for c in candidates]
)
entity_norm = xp.linalg.norm(entity_encodings, axis=1)
if len(entity_encodings) != len(prior_probs):
raise RuntimeError(
Errors.E147.format(
method="predict",
msg="vectors not of equal length",
)
)
# cosine similarity
sims = xp.dot(entity_encodings, sentence_encoding_t) / (
sentence_norm * entity_norm
)
if sims.shape != prior_probs.shape:
raise ValueError(Errors.E161)
scores = prior_probs + sims - (prior_probs * sims)
final_kb_ids.append(
candidates[scores.argmax().item()].entity_
if self.threshold is None
or scores.max() >= self.threshold
else EntityLinker.NIL
random.shuffle(candidates)
# set all prior probabilities to 0 if incl_prior=False
scores = prior_probs = xp.asarray(
[
c.prior_prob if self.incl_prior else 0.0
for c in candidates
]
)
# add in similarity from the context
if self.incl_context:
entity_encodings = xp.asarray(
[c.entity_vector for c in candidates]
)
entity_norm = xp.linalg.norm(entity_encodings, axis=1)
if len(entity_encodings) != len(prior_probs):
raise RuntimeError(
Errors.E147.format(
method="predict",
msg="vectors not of equal length",
)
)
# cosine similarity
sims = xp.dot(entity_encodings, sentence_encoding_t) / (
sentence_norm * entity_norm
)
if sims.shape != prior_probs.shape:
raise ValueError(Errors.E161)
scores = prior_probs + sims - (prior_probs * sims)
final_kb_ids.append(
candidates[scores.argmax().item()].entity_
if self.threshold is None or scores.max() >= self.threshold
else EntityLinker.NIL
)
if not (len(final_kb_ids) == entity_count):
err = Errors.E147.format(
method="predict", msg="result variables not of equal length"
)
raise RuntimeError(err)
return final_kb_ids
def set_annotations(self, docs: Iterable[Doc], kb_ids: List[str]) -> None:

View File

@ -1,4 +1,4 @@
from typing import Callable, Iterable, Dict, Any, Tuple
from typing import Callable, Iterable, Dict, Any, Iterator, Tuple
import pytest
from numpy.testing import assert_equal
@ -6,16 +6,16 @@ from numpy.testing import assert_equal
from spacy import registry, util, Language
from spacy.attrs import ENT_KB_ID
from spacy.compat import pickle
from spacy.kb import Candidate, InMemoryLookupKB, get_candidates, KnowledgeBase
from spacy.kb import Candidate, InMemoryLookupKB, KnowledgeBase
from spacy.lang.en import English
from spacy.ml import load_kb
from spacy.ml.models.entity_linker import build_span_maker
from spacy.ml.models.entity_linker import build_span_maker, get_candidates
from spacy.pipeline import EntityLinker
from spacy.pipeline.legacy import EntityLinker_v1
from spacy.pipeline.tok2vec import DEFAULT_TOK2VEC_MODEL
from spacy.scorer import Scorer
from spacy.tests.util import make_tempdir
from spacy.tokens import Span, Doc
from spacy.tokens import Span, Doc, SpanGroup
from spacy.training import Example
from spacy.util import ensure_path
from spacy.vocab import Vocab
@ -168,7 +168,7 @@ def test_no_entities():
{
"sent_starts": [1, 0, 0, 0, 0],
},
)
),
]
nlp = English()
vector_length = 3
@ -489,11 +489,19 @@ def test_el_pipe_configuration(nlp):
assert doc[1].ent_kb_id_ == ""
assert doc[2].ent_kb_id_ == "Q2"
def get_lowercased_candidates(kb, span):
# Replace the pipe with a new one with with a different candidate generator.
def get_lowercased_candidates(kb: InMemoryLookupKB, span: Span):
return kb.get_alias_candidates(span.text.lower())
def get_lowercased_candidates_batch(kb, spans):
return [get_lowercased_candidates(kb, span) for span in spans]
def get_lowercased_candidates_all(
kb: InMemoryLookupKB, mentions: Iterator[SpanGroup]
):
for doc_mentions in mentions:
yield [
get_lowercased_candidates(kb, doc_mentions[idx])
for idx in range(len(doc_mentions))
]
@registry.misc("spacy.LowercaseCandidateGenerator.v1")
def create_candidates() -> Callable[
@ -501,29 +509,40 @@ def test_el_pipe_configuration(nlp):
]:
return get_lowercased_candidates
@registry.misc("spacy.LowercaseCandidateBatchGenerator.v1")
@registry.misc("spacy.LowercaseCandidateAllGenerator.v1")
def create_candidates_batch() -> Callable[
[InMemoryLookupKB, Iterable["Span"]], Iterable[Iterable[Candidate]]
[InMemoryLookupKB, Iterator[SpanGroup]],
Iterator[Iterable[Iterable[Candidate]]],
]:
return get_lowercased_candidates_batch
return get_lowercased_candidates_all
# replace the pipe with a new one with with a different candidate generator
entity_linker = nlp.replace_pipe(
"entity_linker",
"entity_linker",
config={
"incl_context": False,
"get_candidates": {"@misc": "spacy.LowercaseCandidateGenerator.v1"},
"get_candidates_batch": {
"@misc": "spacy.LowercaseCandidateBatchGenerator.v1"
def test_reconfigured_el(candidates_doc_mode: bool, doc_text: str) -> None:
"""Test reconfigured EL for correct results.
candidates_doc_mode (bool): candidates_doc_mode in pipe config.
doc_text (str): Text to infer.
"""
_entity_linker = nlp.replace_pipe(
"entity_linker",
"entity_linker",
config={
"incl_context": False,
"incl_prior": True,
"candidates_doc_mode": candidates_doc_mode,
"get_candidates": {"@misc": "spacy.LowercaseCandidateGenerator.v1"},
"get_candidates_all": {
"@misc": "spacy.LowercaseCandidateAllGenerator.v1"
},
},
},
)
entity_linker.set_kb(create_kb)
doc = nlp(text)
assert doc[0].ent_kb_id_ == "Q2"
assert doc[1].ent_kb_id_ == ""
assert doc[2].ent_kb_id_ == "Q2"
)
_entity_linker.set_kb(create_kb)
_doc = nlp(doc_text)
assert _doc[0].ent_kb_id_ == "Q2"
assert _doc[1].ent_kb_id_ == ""
assert _doc[2].ent_kb_id_ == "Q2"
# Test individual and doc-wise candidate generation.
test_reconfigured_el(False, text)
test_reconfigured_el(True, text)
def test_nel_nsents(nlp):
@ -1169,18 +1188,19 @@ def test_threshold(meet_threshold: bool, config: Dict[str, Any]):
# create artificial KB
mykb = InMemoryLookupKB(vocab, entity_vector_length=3)
mykb.add_entity(entity=entity_id, freq=12, entity_vector=[6, -4, 3])
mykb.add_alias(
alias="Mahler",
entities=[entity_id],
probabilities=[1 if meet_threshold else 0.01],
)
mykb.add_alias(alias="Mahler", entities=[entity_id], probabilities=[1])
return mykb
# Create the Entity Linker component and add it to the pipeline
entity_linker = nlp.add_pipe(
"entity_linker",
last=True,
config={"threshold": 0.99, "model": config},
config={
"threshold": None if meet_threshold else 1.0,
# Prior for candidate may be 1.0, rendering the our test setting with threshold 1.0 useless otherwise.
"incl_prior": meet_threshold,
"model": config,
},
)
entity_linker.set_kb(create_kb) # type: ignore
nlp.initialize(get_examples=lambda: train_examples)
@ -1191,7 +1211,7 @@ def test_threshold(meet_threshold: bool, config: Dict[str, Any]):
doc = nlp(text)
assert len(doc.ents) == 1
assert doc.ents[0].kb_id_ == entity_id if meet_threshold else EntityLinker.NIL
assert doc.ents[0].kb_id_ == (entity_id if meet_threshold else EntityLinker.NIL)
def test_span_maker_forward_with_empty():
@ -1207,3 +1227,62 @@ def test_span_maker_forward_with_empty():
# just to get a model
span_maker = build_span_maker()
span_maker([doc1, doc2], False)
def test_nel_candidate_processing():
"""Test that NEL handles candidate streams correctly in a set of documents with & without entities as well as empty
documents.
"""
train_data = [
(
"The sky is blue.",
{
"sent_starts": [1, 0, 0, 0, 0],
},
),
(
"They visited New York.",
{
"sent_starts": [1, 0, 0, 0, 0],
"entities": [(13, 21, "GPE")],
},
),
("", {}),
(
"New York is a city.",
{
"sent_starts": [1, 0, 0, 0, 0, 0],
"entities": [(0, 8, "GPE")],
},
),
]
nlp = English()
nlp.add_pipe("sentencizer")
vector_length = 3
train_examples = []
for text, annotation in train_data:
train_examples.append(Example.from_dict(nlp(text), annotation))
def create_kb(vocab):
# create artificial KB
mykb = InMemoryLookupKB(vocab, entity_vector_length=vector_length)
mykb.add_entity(entity="Q60", freq=12, entity_vector=[1, 2, 3])
mykb.add_alias("New York", ["Q60"], [0.9])
return mykb
# Create and train the Entity Linker
entity_linker = nlp.add_pipe("entity_linker", last=True)
entity_linker.set_kb(create_kb)
optimizer = nlp.initialize(get_examples=lambda: train_examples)
for i in range(2):
losses = {}
nlp.update(train_examples, sgd=optimizer, losses=losses)
# Add a custom rule-based component to mimick NER
ruler = nlp.add_pipe("entity_ruler", before="entity_linker")
ruler.add_patterns([{"label": "GPE", "pattern": [{"LOWER": "new york"}]}]) # type: ignore
# this will run the pipeline on the examples and shouldn't crash
nlp.evaluate(train_examples)

View File

@ -2,7 +2,9 @@ from typing import Callable, Protocol, Iterable, Iterator, Optional
from typing import Union, Tuple, List, Dict, Any, overload
from cymem.cymem import Pool
from thinc.types import Floats1d, Floats2d, Ints2d
from .span import Span
from .span_group import SpanGroup
from .token import Token
from ._dict_proxies import SpanGroups
from ._retokenize import Retokenizer
@ -129,6 +131,7 @@ class Doc:
outside: Optional[List[Span]] = ...,
default: str = ...
) -> None: ...
ents_spangroup: SpanGroup
@property
def noun_chunks(self) -> Iterator[Span]: ...
@property

View File

@ -19,6 +19,8 @@ import warnings
from .span cimport Span
from .token cimport MISSING_DEP
from .span_group cimport SpanGroup
from ._dict_proxies import SpanGroups
from .token cimport Token
from ..lexeme cimport Lexeme, EMPTY_LEXEME
@ -701,6 +703,14 @@ cdef class Doc:
"""
return self.text
@property
def ents_spangroup(self) -> SpanGroup:
"""
Returns entities (in `.ents`) as `SpanGroup`.
RETURNS (SpanGroup): All entities (in `.ents`) as `SpanGroup`.
"""
return SpanGroup(self, spans=self.ents, name="ents")
property ents:
"""The named entities in the document. Returns a tuple of named entity
`Span` objects, if the entity recognizer has been applied.